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Noé V, Aubets E, Félix AJ, Ciudad CJ. Nucleic acids therapeutics using PolyPurine Reverse Hoogsteen hairpins. Biochem Pharmacol 2020; 189:114371. [PMID: 33338475 DOI: 10.1016/j.bcp.2020.114371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023]
Abstract
PolyPurine Reverse Hoogsteen hairpins (PPRHs) are DNA hairpins formed by intramolecular reverse Hoogsteen bonds which can bind to polypyrimidine stretches in dsDNA by Watson:Crick bonds, thus forming a triplex and displacing the fourth strand of the DNA complex. PPRHs were first described as a gene silencing tool in vitro for DHFR, telomerase and survivin genes. Then, the effect of PPRHs directed against the survivin gene was also determined in vivo using a xenograft model of prostate cancer cells (PC3). Since then, the ability of PPRHs to inhibit gene expression has been explored in other genes involved in cancer (BCL-2, mTOR, topoisomerase, C-MYC and MDM2), in immunotherapy (SIRPα/CD47 and PD-1/PD-L1 tandem) or in replication stress (WEE1 and CHK1). Furthermore, PPRHs have the ability to target the complementary strand of a G-quadruplex motif as a regulatory element of the TYMS gene. PPRHs have also the potential to correct point mutations in the DNA as shown in two collections of CHO cell lines bearing mutations in either the dhfr or aprt loci. Finally, based on the capability of PPRHs to form triplexes, they have been incorporated as probes in biosensors for the determination of the DNA methylation status of PAX-5 in cancer and the detection of mtLSU rRNA for the diagnosis of Pneumocystis jirovecii. Of note, PPRHs have high stability and do not present immunogenicity, hepatotoxicity or nephrotoxicity in vitro. Overall, PPRHs constitute a new economical biotechnological tool with multiple biomedical applications.
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Affiliation(s)
- Véronique Noé
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Eva Aubets
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Alex J Félix
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain
| | - Carlos J Ciudad
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, & IN2UB, University of Barcelona, 08028 Barcelona, Spain.
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Bandyopadhyay D, Mishra PP. Real-Time Monitoring of the Multistate Conformational Dynamics of Polypurine Reverse Hoogsteen Hairpin To Capture Their Triplex-Affinity for Gene Silencing by smFRET Microspectroscopy. J Phys Chem B 2020; 124:8230-8239. [DOI: 10.1021/acs.jpcb.0c05493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
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Biswas A, Mukhopadhyay S, Singh RS, Kumar A, Rana NK, Koch B, Pandey DS. Manipulating Metallogel Properties by Luminogens and Their Applications in Cell Imaging. ACS OMEGA 2018; 3:5417-5425. [PMID: 30023918 PMCID: PMC6044964 DOI: 10.1021/acsomega.7b01837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Manipulating gelation properties of the isomeric zinc-terpyridine complexes C-1 (nongelator) and C-2 (gelator) using three different luminescent dyes, viz., acridine yellow (AY), ethidium bromide (EB), and azido-boron dipyrromethene, have been described. Hybrid gels created by the combination of C-1, C-2, and above-mentioned dyes have been termed complex-luminogen mixed gels (CLMGs). Ensuing CLMGs have been thoroughly characterized by spectral, morphological, and rheological studies. Cytotoxicity measurements and imaging against breast cancer cell line MDA-MB-231 unveiled that three out of the five CLMGs can be effectively used for cell imaging. Interestingly, direct use of the metal-containing hybrid gels for live cell imaging which is a distinctive approach, has been successfully achieved with significantly encouraging results.
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Affiliation(s)
- Arnab Biswas
- Department of Chemistry,
Institute of Science, and Department of Zoology, Institute
of Science, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Sujay Mukhopadhyay
- Department of Chemistry,
Institute of Science, and Department of Zoology, Institute
of Science, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Roop Shikha Singh
- Department of Chemistry,
Institute of Science, and Department of Zoology, Institute
of Science, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Ashish Kumar
- Department of Chemistry,
Institute of Science, and Department of Zoology, Institute
of Science, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Nishant Kumar Rana
- Department of Chemistry,
Institute of Science, and Department of Zoology, Institute
of Science, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Biplob Koch
- Department of Chemistry,
Institute of Science, and Department of Zoology, Institute
of Science, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Daya Shankar Pandey
- Department of Chemistry,
Institute of Science, and Department of Zoology, Institute
of Science, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
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Charron CL, Hickey JL, Nsiama TK, Cruickshank DR, Turnbull WL, Luyt LG. Molecular imaging probes derived from natural peptides. Nat Prod Rep 2017; 33:761-800. [PMID: 26911790 DOI: 10.1039/c5np00083a] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to the end of 2015.Peptides are naturally occurring compounds that play an important role in all living systems and are responsible for a range of essential functions. Peptide receptors have been implicated in disease states such as oncology, metabolic disorders and cardiovascular disease. Therefore, natural peptides have been exploited as diagnostic and therapeutic agents due to the unique target specificity for their endogenous receptors. This review discusses a variety of natural peptides highlighting their discovery, endogenous receptors, as well as their derivatization to create molecular imaging agents, with an emphasis on the design of radiolabelled peptides. This review also highlights methods for discovering new and novel peptides when knowledge of specific targets and endogenous ligands are not available.
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Affiliation(s)
- C L Charron
- Department of Chemistry, The University of Western Ontario, London, Canada.
| | - J L Hickey
- Department of Chemistry, The University of Western Ontario, London, Canada.
| | - T K Nsiama
- London Regional Cancer Program, Lawson Health Research Institute, London, Canada
| | - D R Cruickshank
- Department of Chemistry, The University of Western Ontario, London, Canada.
| | - W L Turnbull
- Department of Chemistry, The University of Western Ontario, London, Canada.
| | - L G Luyt
- Department of Chemistry, The University of Western Ontario, London, Canada. and Departments of Oncology and Medical Imaging, The University of Western Ontario, London, Canada and London Regional Cancer Program, Lawson Health Research Institute, London, Canada
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Golubev O, Lönnberg T, Lönnberg H. Metal-Ion-Binding Analogs of Ribonucleosides: Preparation and Formation of Ternary Pd2+and Hg2+Complexes with Natural Pyrimidine Nucleosides. Helv Chim Acta 2013. [DOI: 10.1002/hlca.201300042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kalachova L, Pohl R, Bednárová L, Fanfrlík J, Hocek M. Synthesis of nucleosides and dNTPs bearing oligopyridine ligands linked through an octadiyne tether, their incorporation into DNA and complexation with transition metal cations. Org Biomol Chem 2013; 11:78-89. [PMID: 23090069 DOI: 10.1039/c2ob26881g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Modified nucleosides (dA(R)s and dC(R)s) bearing bipyridine or terpyridine ligands attached through an octadiyne linker were prepared by single-step aqueous-phase Sonogashira cross-coupling of 7-iodo-7-deaza-2'-deoxyadenosine and 5-iodo-2'-deoxycytidine with the corresponding bipyridine- or terpyridine-octadiynes and were triphosphorylated to the corresponding nucleoside triphosphates (dA(R)TPs and dC(R)TPs). The modified dN(R)TPs were successfully incorporated into the oligonucleotides by primer extension experiment (PEX) using different DNA polymerases and the PEX products were used for post-synthetic complexation with divalent metal cations. The complexation of these DNAs containing flexibly-tethered ligands was compared with the previously reported ones bearing rigid acetylene-linked ligands suggesting the possible formation of both inter- and intra-strand complexes with Ni(2+) or Fe(2+).
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Affiliation(s)
- Lubica Kalachova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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